Technical Abstract: As part of the NSF-sponsored Soybean Functional Genomics Program, we have accumulated a set of unique genes from a larger collection of soybean 5'ESTs. The current unigene collection (or tentatively unique sequences) represents 36,864 low redundancy cDNA clones. These include reracked libraries Gm-r1070 (a set of 9216 cDNA clones from various stages of immature cotyledons, flowers, pods, and seed coats); Gm-r1021 plus Gm-r1083 (a set of approximately 9216 cDNA clones from 8-day old seedling roots, seedling roots inoculated with B. japonicum, whole seedlings, and 2 month old roots); Gm-r1088 and Gm-r1089 (a collection of 9216 cDNA clones from a number of libraries made from cotyledons and hypocotyls of germinating seedlings and leaves and other plant parts subjected to various pathogens or environmental stress conditions). Functional assignments of clones were inferred by matching the BLASTX hits of the 5' and 3' sequences to the non-redundant databases. The inserts were amplified from each clone by PCR and were spotted onto glass slides for microarray analysis. Initially three arrays were produced, each with approximately 9,216 cDNAs for a total of 27,648 genes. Currently we are producing two arrays with approximately 18,432 cDNAs each, for a total of 36,864 genes. We are currently using these arrays to study gene expression during soybean seed development (see poster by Jones, et. al.); during reprogramming of cotyledon cells associated with induction of somatic embryos in soybean tissue culture (Thibaud-Nissen, et al., Plant Physiol, 132:118-136, 2003), and to analyze isogenic lines containing mutations in the flavonoid pathway.